Abstract Irreproducibility of research data due to misidentification or propagated errors within cell lines impacts $3.7bn research funding in the US each year. Moreover, it is not easy to rapidly and inexpensively monitor the genomic composition and evolution of a cell line during its long-term culture. The project concerns development of a technology that integrates extraction of DNA from in vitro cultured cell lines with single molecule analysis of the genomes present in the population of cells. Phase 1 of the project will demonstrate the feasibility of acquiring sequence, structural and epigenomic information robust enough to identify and characterize cell lines.